Summary:
On Affymetrix gene expression microarrays, a given gene may be detected by multiple probe sets which may deliver inconsistent or even contradictory measurements.
Therefore, obtaining an unambiguous expression estimate of a pre-specified gene can be nontrivial.
We developed scoring methods to assess each probe set for specificity, coverage, and degradation resistance.
We used these scores to select the optimal probe set for each gene, and thus create a simple one-to-one mapping between gene and probe set.